One of the features of drug design in the -omics era is the shift from target- and structure-based to function-based drug discovery, when the active compound is identified simultaneously or before the mechanism of action.
A new report in Nature Chemical Biology describes an interesting blend of small molecule high-throughput screening with genetic screening via synthetic lethality. As one might guess, the approach is dealing with cellular death. Traditional ‘simple’ genetic screen identifies individual genes that are critical for cell survival. The principle of synthetic lethality is somewhat different. Scientists seek gene pairs or networks that are crucial in combination but which could be silenced individually without jeopardizing essential cellular functions. Previously it was applied for the discovery of anticancer therapeutics. This time the team from Harvard Medical School aimed at Staphyllococcus aureus.
In the previous paper authors have narrowed down the number of S. aureus candidate genes by pharmacological inhibition of wall teichoic acid (WTA) biosynthesis and checking the viability of S. aureus transposon library. WTA, a major component of bacterial cell wall, per se is not critical for survival but when some other genes are switched off, the cells are dying or lose their ability to divide.
In the new study the authors reversed the experiment, they took three S. aureus strains (WT, WTA-deficient, and D-alanylation–deficient) and screened ~28k compound library against them. So basically they probed synthetic lethality with small molecules instead of directly messing with genes. The compounds that selectively killed mutant but not WT strains were ranked by principle component analysis (PCA). Frankly, for two-dimentional data they could as well just stare at the scatter plots, but the approach could be a useful ranking method for more complex dataset. Eventually, they identified amsacrine as a primary hit selectively killing WTA-deficient S. aureus.
To optimize the hit and eliminate eukaryotic topoisomerase off-target activity of amsacrine, the authors pushed the methoxy substituent one carbon further from the heterocyclic core (they report the synthesis of only one compound, isn’t it the essence of rational design?). The real gem of the paper is the target identification experiments. As it often happens, the traditional approach to identify the target genes was unsuccessful. So the authors turned again to synthetic lethality! The whole target validation and elucidation of the mechanism is a beautiful example of experiment design and creativity.
Although the discovery required quite some troubleshooting along the way, the described pharmacogenomic approach has an enourmous potential as a drug discovery platform. If one could change the readout from cell death to something less dramatic, such screening would facilitate the study of drug-drug interaction and/or polypharmacology far beyond antibiotic area.